Chris Rhodes Week 5: Difference between revisions
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'''Rooted Tree''' | '''Rooted Tree''' | ||
[[Image:CHR_Image3_20110928.gif | Subject 3 Rooted Tree]] | [[Image:CHR_Image3_20110928.gif | Subject 3 Rooted Tree]] | ||
Based on both the rooted and unrooted trees you can see that subject 3 had very high diversity and divergence. The rooted tree shows a large vertical distance between its two ends and a large amount of branching with no branch being prominent. The clones seem to cluster together based on their visit number to create the various branches and show little similarity with clones outside of their own visit.The only exceptions to this pattern are some of the clones of visit 4 who share greater similarities to visit 1 or 3 clones rather than with other visit 4 clones. However, this overall pattern is indicative of an immune response in which there is no selection happening for or against change in the amino acid sequence which results in indiscriminate mutations. | |||
*Subject 7 | *Subject 7 | ||
'''Unrooted Tree''' | '''Unrooted Tree''' |
Revision as of 16:50, 28 September 2011
Methods
- To create ClustalW alignments and phylogenetic trees for the chosen subjects(3,7,8,11,12, and 13) each subject's sequence datawas uploaded onto Workbench each as a separate session.
- For each subject's clones a ClustalW alignment was run using default parameters to generate both the rooted and unrooted phylogenetic trees.
- Subject 3
Rooted Tree Based on both the rooted and unrooted trees you can see that subject 3 had very high diversity and divergence. The rooted tree shows a large vertical distance between its two ends and a large amount of branching with no branch being prominent. The clones seem to cluster together based on their visit number to create the various branches and show little similarity with clones outside of their own visit.The only exceptions to this pattern are some of the clones of visit 4 who share greater similarities to visit 1 or 3 clones rather than with other visit 4 clones. However, this overall pattern is indicative of an immune response in which there is no selection happening for or against change in the amino acid sequence which results in indiscriminate mutations.
- Subject 7
- Subject 8
- Subject 11
- Subject 12
- Subject 13
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